rs5755495

Variant names:

• chr22-35002849-C-G
• rs5755495
• ENST00000668433.1:n.14G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-35002849-C-G
• chr22-35002849-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668433.1(LINC02885):​n.14G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,872 control chromosomes in the GnomAD database, including 29,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (29309 hom., cov: 31)
  • Exomes 𝑓: 0.55 (2 hom.)
• Consequence: LINC02885 ENST00000668433.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 publications found

Genes affected

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02885	ENST00000668433.1	n.14G>C		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93241 AN: 151730 Hom.: 29274 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.601

GnomAD4 exome AF: 0.545 AC: 12 AN: 22 Hom.: 2 Cov.: 0 AF XY: 0.550 AC XY: 11 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 8 AN: 16

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.615 AC: 93335 AN: 151850 Hom.: 29309 Cov.: 31 AF XY: 0.619 AC XY: 45918 AN XY: 74204

African (AFR) AF: 0.734 AC: 30404 AN: 41404

American (AMR) AF: 0.577 AC: 8797 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1851 AN: 3468

East Asian (EAS) AF: 0.688 AC: 3541 AN: 5146

South Asian (SAS) AF: 0.780 AC: 3755 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6085 AN: 10538

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36957 AN: 67912

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.591 Hom.: 3329

Bravo AF: 0.617

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5755495; hg19: chr22-35398839;